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splatter

Simple Simulation of Single-cell RNA Sequencing Data


Bioconductor version: Release (3.18)

Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.

Author: Luke Zappia [aut, cre] , Belinda Phipson [aut] , Christina Azodi [ctb] , Alicia Oshlack [aut]

Maintainer: Luke Zappia <luke at lazappi.id.au>

Citation (from within R, enter citation("splatter")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("splatter")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("splatter")
An introduction to the Splatter package HTML R Script
Splat simulation parameters HTML R Script
splatPop simulation HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.26.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-3 + file LICENSE
Depends R (>= 4.0), SingleCellExperiment
Imports BiocGenerics, BiocParallel, checkmate (>= 2.0.0), crayon, edgeR, fitdistrplus, grDevices, locfit, matrixStats, methods, rlang, S4Vectors, scuttle, stats, SummarizedExperiment, utils, withr
System Requirements
URL https://github.com/Oshlack/splatter
Bug Reports https://github.com/Oshlack/splatter/issues
See More
Suggests BASiCS(>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), IRanges, igraph, knitr, limSolve, lme4, magick, mfa, phenopath, progress, preprocessCore, pscl, rmarkdown, scales, scater(>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave
Linking To
Enhances
Depends On Me
Imports Me SCRIP
Suggests Me mastR, NewWave, scone, scPCA, SummarizedBenchmark
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package splatter_1.26.0.tar.gz
Windows Binary splatter_1.26.0.zip (64-bit only)
macOS Binary (x86_64) splatter_1.26.0.tgz
macOS Binary (arm64) splatter_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/splatter
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/splatter
Bioc Package Browser https://code.bioconductor.org/browse/splatter/
Package Short Url https://bioconductor.org/packages/splatter/
Package Downloads Report Download Stats